Neuropeptides form the largest and most diverse class of signaling molecules in the brain that are involved in the integration of complex physiological processes and behaviors. Functionally related neurons commonly express overlapping yet different sets of peptides, which enables the coordination of intricate spatiotemporal patterns of activity in target cells. Due to the high complexity in vertebrate neuronal systems, invertebrate systems have been exploited as alternative model systems to investigate the significance of the use of multiple peptide messengers for neuronal communication. The identification of the peptide messengers contained in neurons is generally tedious due to their high structural diversity. In the present study, we use direct MALDI-MS analysis for the screening of peptide profiles of singly dissected neurons in conjunction with post-source decay analysis and tandem MS for the structural elucidation of molecular species of interest.